Tests Cross-Platform #172

Workflow file for this run

.github/workflows/tests-conda.yml at 59966e5

	name: Tests Cross-Platform

	on:
	workflow_dispatch:
	pull_request:
	branches:
	- dev
	- master
	push:
	branches:
	- dev
	- master

	jobs:
	build:
	runs-on: windows-latest
	strategy:
	max-parallel: 5
	matrix:
	python-version: ["3.8", "3.9", "3.10"]
	timeout-minutes: 120

	steps:

	- uses: actions/checkout@v2

	- name: Set up JDK 17
	uses: actions/setup-java@v2
	with:
	java-version: '17'
	distribution: 'temurin'

	- name: Print JAVA_HOME and PATH
	run: \|
	echo "JAVA_HOME: $env:JAVA_HOME"
	echo "PATH: $env:PATH"
	shell: pwsh

	- name: Set JDK_HOME environment variable
	run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
	shell: bash


	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-activate-base: false
	activate-environment: pathml
	# environment-file: '.github/ci-environments/env-py39.yml'
	environment-file: .github/ci-environments/env-py${{ matrix.python-version == '3.10' && '310' \|\| matrix.python-version == '3.9' && '39' \|\| '38' }}.yml
	mamba-version: "*"
	python-version: ${{ matrix.python-version }}

	# - name: Install JavaBridge and other dependencies
	# shell: bash -l {0}
	# run: \|
	# pip install python-javabridge

	- name: Run Python script to find JVM path
	shell: bash -l {0}
	run: \|
	python -c "import javabridge; print('javabridge.locate.find_javahome():', javabridge.locate.find_javahome()); print('javabridge.jutil._find_jvm_windows():', javabridge.jutil._find_jvm_windows())"

	- name: Print JAVA_HOME and PATH Second
	run: \|
	echo "JAVA_HOME: $env:JAVA_HOME"
	echo "PATH: $env:PATH"
	shell: pwsh


	- name: Download and Setup OpenSlide
	run: \|
	# $zipFile = "openslide-win64-20231011.zip"
	$zipFile = "openslide-win64-20230414.zip"
	$extractPath = Join-Path $env:GITHUB_WORKSPACE "openslide-binaries"
	# Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/$zipFile" -OutFile $zipFile
	Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20230414/$zipFile" -OutFile $zipFile
	Expand-Archive -Path $zipFile -DestinationPath $extractPath
	# $binPath = Join-Path $extractPath "openslide-win64-20231011/bin"
	$binPath = Join-Path $extractPath "openslide-win64-20230414/bin"
	Write-Host "Adding to PATH: $binPath"
	echo "OPENSLIDE_PATH=$binPath" \| Out-File -Append -FilePath $env:GITHUB_ENV
	# echo "$binPath" \| Out-File -Append -FilePath $env:GITHUB_PATH
	shell: pwsh

	# Optional: List files in OpenSlide bin directory to verify
	- name: List files in OpenSlide bin directory
	run: \|
	Get-ChildItem -Path $env:OPENSLIDE_PATH
	shell: pwsh
	env:
	OPENSLIDE_PATH: ${{ env.OPENSLIDE_PATH }}

	- name: Conda info
	shell: bash -l {0}
	run: \|
	conda info
	conda list

	- name: Install PathML
	shell: bash -l {0}
	run: pip install -e .

	- name: Install torchvision
	shell: bash -l {0}
	run: pip install torchvision==0.14.1

	- name: Set OPENSLIDE_PATH
	run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV
	shell: pwsh

	- name: Test other modules with pytest and generate coverage
	shell: bash -l {0}
	run: \|
	# coverage run --data-file=.coverage_others -m pytest -m "not slow and not exclude"
	coverage run --data-file=.coverage_others -m pytest -v -m "not slow and not exclude"
	continue-on-error: true

	# steps:
	# - uses: actions/checkout@v2

	# - name: Set up JDK 17
	# uses: actions/setup-java@v2
	# with:
	# java-version: '17'
	# distribution: 'temurin'
	# id: setup-java

	# - name: Debug JAVA_HOME
	# run: \|
	# echo $env:JAVA_HOME
	# echo $env:PATH
	# shell: pwsh

	# - name: Set JDK_HOME environment variable
	# run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
	# shell: bash

	# - name: Print JAVA_HOME and JDK_HOME
	# run: \|
	# echo "JAVA_HOME: $env:JAVA_HOME"
	# echo "JDK_HOME: $env:JDK_HOME"
	# shell: pwsh

	# - name: Download and Setup OpenSlide
	# run: \|
	# # $zipFile = "openslide-win64-20231011.zip"
	# $zipFile = "openslide-win64-20230414.zip"
	# $extractPath = Join-Path $env:GITHUB_WORKSPACE "openslide-binaries"
	# # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/$zipFile" -OutFile $zipFile
	# Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20230414/$zipFile" -OutFile $zipFile
	# Expand-Archive -Path $zipFile -DestinationPath $extractPath
	# # $binPath = Join-Path $extractPath "openslide-win64-20231011/bin"
	# $binPath = Join-Path $extractPath "openslide-win64-20230414/bin"
	# Write-Host "Adding to PATH: $binPath"
	# echo "OPENSLIDE_PATH=$binPath" \| Out-File -Append -FilePath $env:GITHUB_ENV
	# # echo "$binPath" \| Out-File -Append -FilePath $env:GITHUB_PATH
	# shell: pwsh

	# # Optional: List files in OpenSlide bin directory to verify
	# - name: List files in OpenSlide bin directory
	# run: \|
	# Get-ChildItem -Path $env:OPENSLIDE_PATH
	# shell: pwsh
	# env:
	# OPENSLIDE_PATH: ${{ env.OPENSLIDE_PATH }}


	# # - name: Download and Setup OpenSlide
	# # run: \|
	# # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip"
	# # # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
	# # # echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" \| Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
	# # shell: pwsh

	# # - name: Extract OpenSlide Binaries
	# # run: \|
	# # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
	# # $binPath = Join-Path ${{ github.workspace }} "openslide-binaries/openslide-win64-20231011/bin"
	# # Write-Host "Adding to PATH: $binPath"
	# # echo "$binPath" \| Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
	# # shell: pwsh

	# # - name: List files in OpenSlide bin directory
	# # run: \|
	# # $binPath = Join-Path ${{ github.workspace }} "openslide-binaries/openslide-win64-20231011/bin"
	# # Get-ChildItem -Path $binPath
	# # shell: pwsh


	# - name: Check PATH
	# run: \|
	# # echo $env:JAVA_HOME
	# echo $env:PATH
	# shell: pwsh

	# - name: Setup Miniconda
	# uses: conda-incubator/setup-miniconda@v2
	# with:
	# auto-activate-base: false
	# activate-environment: pathml
	# # environment-file: '.github/ci-environments/env-py39.yml'
	# environment-file: .github/ci-environments/env-py${{ matrix.python-version == '3.10' && '310' \|\| matrix.python-version == '3.9' && '39' \|\| '38' }}.yml
	# mamba-version: "*"
	# python-version: ${{ matrix.python-version }}

	# - name: Debugging
	# shell: bash -l {0}
	# run: \|
	# echo "Checking the status of mamba..."
	# mamba --version
	# echo "Checking the available disk space..."
	# df -h

	# - name: Conda info
	# shell: bash -l {0}
	# run: \|
	# conda info
	# conda list

	# - name: Install PathML
	# shell: bash -l {0}
	# run: pip install -e .

	# - name: Install torchvision
	# shell: bash -l {0}
	# run: pip install torchvision==0.14.1

	# # - name: Download and Setup OpenSlide
	# # run: \|
	# # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip"
	# # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
	# # echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" \| Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
	# # shell: pwsh

	# - name: Set OPENSLIDE_PATH
	# run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV
	# shell: pwsh

	# - name: Check PATH
	# run: \|
	# # echo $env:JAVA_HOME
	# echo $env:PATH
	# shell: pwsh

	# # - name: Test tile_stitcher with pytest and generate coverage
	# # shell: bash -l {0}
	# # run: \|
	# # coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py
	# # continue-on-error: true

	# # - name: Test other modules with pytest and generate coverage
	# # shell: bash -l {0}
	# # run: \|
	# # # coverage run --data-file=.coverage_others -m pytest -m "not slow and not exclude"
	# # coverage run --data-file=.coverage_others -m pytest -v -m "not slow and not exclude"
	# # continue-on-error: true

	# - name: Increase Test Verbosity and Add Resource Monitoring
	# run: \|
	# # Adding resource monitoring for diagnosis
	# Start-Process -FilePath "powershell" -ArgumentList "Get-Process \| Sort-Object -Property CPU -Descending \| Select-Object -First 10; Get-Counter '\Memory\Available MBytes', '\Processor(_Total)\% Processor Time';" -NoNewWindow -PassThru
	# coverage run --data-file=.coverage_others -m pytest -v -m "not slow and not exclude"
	# continue-on-error: true
	# shell: pwsh

	# - name: Check System Resources After Tests
	# run: \|
	# Get-Process \| Sort-Object -Property CPU -Descending \| Select-Object -First 10
	# Get-Counter '\Memory\Available MBytes', '\Processor(_Total)\% Processor Time'
	# shell: pwsh


	# name: Tests Cross-Platform

	# on:
	# workflow_dispatch:
	# pull_request:
	# branches:
	# - dev
	# - master
	# push:
	# branches:
	# - dev
	# - master

	# jobs:
	# build:
	# runs-on: windows-latest # Use Ubuntu if you're building on Linux, or keep windows-latest if you're targeting Windows.
	# strategy:
	# max-parallel: 5
	# matrix:
	# python-version: [3.9]
	# timeout-minutes: 60

	# steps:
	# - uses: actions/checkout@v2

	# - name: Set up JDK 17
	# uses: actions/setup-java@v2
	# with:
	# java-version: '17'
	# distribution: 'temurin' # Use 'temurin' for Eclipse Temurin distribution
	# id: setup-java

	# - name: Debug JAVA_HOME
	# run: \|
	# echo $env:JAVA_HOME
	# echo $env:PATH
	# shell: pwsh

	# - name: Set JDK_HOME environment variable
	# shell: bash
	# run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV

	# - name: Print JAVA_HOME and JDK_HOME
	# run: \|
	# echo "JAVA_HOME: $env:JAVA_HOME"
	# echo "JDK_HOME: $env:JDK_HOME"
	# shell: pwsh

	# - name: vcpkg build
	# uses: johnwason/vcpkg-action@v6
	# id: vcpkg
	# with:
	# pkgs: openslide
	# triplet: x64-windows
	# token: ${{ github.token }}
	# github-binarycache: true

	# - name: Setup Miniconda
	# uses: conda-incubator/setup-miniconda@v2
	# with:
	# auto-activate-base: false
	# activate-environment: pathml
	# environment-file: '.github/ci-environments/env-py39.yml' # Directly specify the env-py39.yml file
	# mamba-version: "*"
	# python-version: ${{ matrix.python-version }}

	# - name: Debugging
	# shell: bash -l {0}
	# run: \|
	# echo "Checking the status of mamba..."
	# mamba --version
	# echo "Checking the available disk space..."
	# df -h

	# - name: Conda info
	# shell: bash -l {0}
	# run: \|
	# conda info
	# conda list

	# - name: Install PathML
	# shell: bash -l {0}
	# run: pip install -e .

	# # - name: Install python-spams
	# # shell: bash -l {0}
	# # run: pip install spams

	# - name: Install torchvision
	# shell: bash -l {0}
	# run: pip install torchvision==0.14.1

	# - name: Set up vcpkg
	# uses: lukka/run-vcpkg@v10
	# with:
	# # Setup vcpkg directory
	# vcpkgDirectory: '${{ github.workspace }}/vcpkg'
	# # Clone vcpkg repo
	# setupOnly: true

	# - name: Install OpenSlide with vcpkg
	# run: \|
	# ./vcpkg/vcpkg install openslide
	# working-directory: ${{ github.workspace }}

	# - name: Test tile_stitcher with pytest and generate coverage
	# shell: bash -l {0}
	# run: \|
	# # COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py
	# coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py

	# - name: Test other modules with pytest and generate coverage
	# shell: bash -l {0}
	# run: coverage run --data-file=.coverage_others -m pytest -m "not slow and not exclude"
	# # COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"

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Tests Cross-Platform #172

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Tests Cross-Platform #172

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